PROJECT SUMMARY Sex-bias exists in the human genome in DNA content and gene expression. The human X and Y chromosomes are useful tools for inferring human demography, and crucial for our understanding of human health. However, despite the genomics era, X and Y chromosomes are still vastly underutilized, especially in a genome-wide context. My research has focused on the integration of these chromosomes to build comprehensive analyses of human history and utilizing an evolutionary approach to characterize sex-bias in gene expression. Using comparative genomics, we have shown that the human Y chromosome has lost nearly 90% of the gene content it once shared with the X, but that natural selection is still active on the human Y. Further, we showed that, only when analyzing all regions of the genome together (autosomes, X chromosomes, and the non-recombining and uni-parentally inherited Y chromosome and mtDNA), could one infer the relative strength of sex-biased demography along with natural selection, acting across the human genome. Further, our research supports the theory that the human dosage-compensation mechanism via X- inactivation, evolved step-wise, in a gene-by-gene specific manner on the X chromosome in response to loss of functional Y-linked genes. This project will include a three-pronged approach to utilizing and studying sex chromosome variation across humans. First, we will focus on development and extensive testing of novel methodology for accurately accounting for technical variation that affects alignment and variant calling on the sex chromosomes. Current alignment pipelines do not account for the shared homology between the X and Y chromosome, resulting in mis-mapping of reads between the sex chromosomes and reduced power for variant calling. Our methodology will incorporate sex chromosome biology to improve variant calling on the sex chromosomes. Second, we will study truly genome-wide patterns of variation (autosomes, X chromosome, Y chromosome, and mtDNA) among multiple populations in Kenya. Populations in Africa are the most diverse in the world, and representation of that diversity is conspicuously absent from global population studies. In collaboration with anthropologists, who are studying, cultural variation, we will assess how genetically diverse individuals are, and use patterns of variation across the sex chromosomes and autosomes to infer recent and ancient demography in these populations. Third, we will study gene expression variation (with an emphasis on X-linked gene expression and X-inactivation) between the sexes, and between populations in the human placenta. The placenta is the one organ routinely expelled from the body that also provides a crucial interface during development, and is not studied in current large-scale tissue expression projects. In collaboration with a long-term pregnancy outcome study we will generate and comprehensively analyze population-specific sex- bias in the human placenta. This work will improve methodology for studying sex-linked variation, provide estimates of sex-biased human demography, and elucidate sex-biased expression in the human placenta.